The major histocompatibility complex (MHC) plays key roles in controlling both adaptive and innate immune systems. In the adaptive immune system, both MHC class I and class II antigens recognize, bind and present peptides to cytotoxic and helper T-cells, respectively, and initiate cell-to-cell communication between antigen presenting cells and T-cells by forming immunological synapses and activating both subtypes of T-cells for cellular and humoral immune systems. More recently, a variety of host restriction genes have been identified in humans and mammals that modulate retrovirus infectivity, replication, assembly and/or cross-species transmission. One of these host encoded genes, Apolipoprotein B mRNA-editing enzyme catalytic (APOBEC2) is capable of terminally editing feline foamy virus in the absence of virally-encoded Bet protein, but not in its presence, similar to the interplay of APOBEC3 and the HIV-encoded protein Vif. The editing capacity of APOBEC3 appears to be species specific and limits cross-species transmission of retroviruses. To identify and characterize APOBEC genes in the feline genome, we attempted APOBEC-related sequences in the scaffolds of the partial (2x) genome sequence of the domestic cat and compared these phylogenetically to their human and dog counterparts. In addition, we determined approximately 50 kbp APOBEC3 region from three fosmid clones. (A) Comparative Genomic Structure of the MHC Comparisons of the genomic structure of three mammalian MHC, human leukocyte antigens (HLA), canine dog leukocyte antigens (DLA), and feline leukocyte antigens (FLA) revealed remarkable structural differences between HLA and the other two MHC. The 4.6 Mb HLA sequence was compared with the 3.9 Mb DLA sequence from two supercontigs generated by 7x whole genome shotgun assembly and 3.3 Mb FLA draft sequence. For FLA, we confirm that: (i) feline FLA was split into two pieces within the TRIM gene family found in human HLA; (ii) class I, II, and III regions were placed in the pericentrocentric region of the long arm of chromosome B2; and (iii) remaining FLA was located in subtelomeric region of the short arm of chromosome B2. The exact same chromosome break was found in canine DLA structure, where class I, II, and III regions were placed in a percentromeric region of chromosome 12, while the remaining region was located in a subtelomeric region of chromosome 35, suggesting this chromosome break occurred once before a split of felid and canid more than 55 MYA. However, significant differences were found in the content of genes in both pericentromeric and subtelomeric regions in DLA and FLA, the gene number and amplicon structure of class I genes plus two other class I genes found on two additional chromosomes; canine chromosome 7 and 18, suggests the dynamic nature in the evolution of MHC class I genes. (B) Sequences, Annotation and Single Nucleotide Polymorphism (SNP) of the MHC in the Domestic Cat Two sequences of the MHC regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55 - 80 MYA) and followed by a chromosomal inversion were determined by bacterial artificial chromosome (BAC) shotgun sequencing. Gene annotation of this MHC was completed and identified 317 possible coding regions (128 human homologues, possible functional genes and 189 pseudo/unidentified genes) by GENSCAN, BLASTN, and BLASTP programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens), nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and LMP2/LMP7.TAP1/TAP2), 52 class III genes, 19 class I antigens (FLAI-A to FLAI-S). Two class I genes (FLAI-H, I-K) were transcribed in a feline fibroblast cell line and one (FLAI-E) had a peptide binding site structure similar to the classical class I gene. The second region spans 0.362 Mbp sequence encoding no class I genes and 18 framework genes, including three olfactory receptor genes. One previously identified feline endogenous retrovirus, a baboon retrovirus derived sequence (ECE1) and two new endogeneous retrovirus sequences, both of which showed high sequence similarity to brown bat endogeneous retrovirus (FERVmlu1, FERVmlu2) were found within a 100 Kbp interval in the middle of class I region. MHC SNPs were examined based on comparisons of this BAC sequence and MHC homozygous 2 X whole genome scan (WGS) sequences and found that 11,654 SNPs in 2.84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in 2 X WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp). (C) Innate Defense Mechanisms Against Exogenous and Endogenous Retroviruses in the Domestic Cat. APOBEC3 anti retroviral function against three feline viruses (FIV, FeLV, Formy Virus). In order to find functions of APOBEC3 molecules, we have isolated three fosmid clones which cover approximately 50 kpb sequence on feline A3 locus using web-based fosmid cloning system established in feline genome browser (GARField). High quality and complete DNA sequences of these three fosmid clones were determined by transposon insertion and Sanger methods using Biomek Fx/ ABI3730XL DNA sequencer and Phred/Phrap/Consed applications. We found that a. Four A3C genes complete genes exist in head-tail fashions. b. Each A3Ca, A3Cb, A3c, A3H genes are transcribed and produce A3C molecules. c. Each molecules has differential antiretroviral activities. For example, A3a, A3b, A3c strongly suppress delta-bet formy virus infection, however no effects on infections of delta-vif FIV nor FeLV A3H suppress delta-vif FIV moderately but no effects on delta-bet formy virus nor FeLV. d. Read-through alternative splicing generate hybrid two catalytic domain A3CH molecules using cryptic splicing donor site overlapped with TGA stop codon of A3Cc and join exon 2 of A3H with in frame translation of A3H part of this hybrid molecule. This A3CH molecule have strong anti-viral activities against both delta-vif FIV and FeLV but not against delta-bet formy virus. e. Excess of nonsynonymous substitutions in A3C genes were found by SNP analyses of nine cat breeds. These amino acid positions are located on sites which involved in tetramer and dimer formation. One of these sites are found to be the same site which determine host specific interactions between human and african green monkey APOBEC3G and Vif in HIV and SIVagm. Site direct mutagenesis are now planned to examine the effects of these amino acid substitutions against FIV, FeLV and formy virus infections.